I am having the same problem as David but I tried even further. I tried using rEFInd, which used to work before I installed Qubes but this time it doesn't list any options to load either Windows 10 or Debian (I had dual booting with these two before installing Qubes in another partition, planing to have a third OS for testing/learning purposes). Qubes discontinued its version for Live USB (it doesn't support it anymore so I discarded it).
I tried EVERY SINGLE THING. I even loaded "Repair > Command Prompt" from a Windows 10 Repair USB Drive to run "bootrec.exe /FixMbr" and "bootrec.exe /FixBoot" and "bootrec /RebuildBcd" (which used to work before - yeah I learned a lot from my first dual booting experience), and although it printed "successful" the problem remained the same this time, after rebooting the machine (only Qubes showing up for loading). Then I also tried "bootsect /nt60 c: /mbr" (didn't work) and I tried "bootsect /nt60 ALL /mbr" (also nothing).
So, I reinstalled Windows 10 (during the process I confirm current Windows would be renamed to Windows.old etc, etc.) and all files were copied and installed and everything went well but when it finally finished for rebooting, no Windows to load. I tried the same with Debian, reinstalling it again to its partition, and all went well but no booting for this either. Qubes completed "sealed" the MBR and EFI zones. Those cannot be re-written!
In fact, I even went further resetting my BIOS, following HP instructions (my laptop is a "HP ENVY dv7" and tried to updated the BIOS again from a combination of instructions (pressing power button for 2/3 seconds while pressing Windows Key together with B or V) to start the process, which I remember worked once before, but for some reason is not working anymore. So it seems Qubes re-wrote something in my BIOS as well. Unbelievable. At this moment everything I get now is "Missing operating system" on my screen. I know my files are still there. The partitions are still there. Windows and Debian with all my personal files are still there. But I cannot access them. I simply can't. Qubes gives me only one option: reinstalling itself. It is like a malware which took reign of my laptop.
Using another laptop (thanks God I have another one), I searched for "how to uninstall Qubes", "how to remove Qubes" etc. but all I get are pages talking about how to remove/reinstalling Qubes's templates. There is nothing about removing the OS itself. How can that be?
Please, if anybody knows anything that can help me restoring my Windows I would appreciate very much. Thanks!